OpenRaiser/Intern-Atlas huggingface dataset:
Tensor Generalized Approximate Message Passing
Venue: arXiv cs.LG 2025
Year: 2025

We propose a tensor generalized approximate message passing (TeG-AMP) algorithm for low-rank tensor inference, which can be used to solve tensor completion and decomposition problems. We derive TeG-AMP algorithm as an approximation of the sum-product belief propagation algorithm in high dimensions where the central limit theorem and Taylor series approximations are applicable. As TeG-AMP is developed based on a general TR decomposition model, it can be directly applied to many low-rank tensor types. Moreover, our TeG-AMP can be simplified based on the CP decomposition model and a tensor simplified AMP is proposed for low CP-rank tensor inference problems. Experimental results demonstrate that the proposed methods significantly improve recovery performances since it takes full advantage of tensor structures.
SandboxEval: Towards Securing Test Environment for Untrusted Code
Venue: arXiv cs.CR 2025
Year: 2025

While large language models (LLMs) are powerful assistants in programming tasks, they may also produce malicious code. Testing LLM-generated code therefore poses significant risks to assessment infrastructure tasked with executing untrusted code. To address these risks, this work focuses on evaluating the security and confidentiality properties of test environments, reducing the risk that LLM-generated code may compromise the assessment infrastructure. We introduce SandboxEval, a test suite featuring manually crafted test cases that simulate real-world safety scenarios for LLM assessment environments in the context of untrusted code execution. The suite evaluates vulnerabilities to sensitive information exposure, filesystem manipulation, external communication, and other potentially dangerous operations in the course of assessment activity. We demonstrate the utility of SandboxEval by deploying it on an open-source implementation of Dyff, an established AI assessment framework used to evaluate the safety of LLMs at scale. We show, first, that the test suite accurately describes limitations placed on an LLM operating under instructions to generate malicious code. Second, we show that the test results provide valuable insights for developers seeking to harden assessment infrastructure and identify risks associated with LLM execution activities.
FUSE : A Ridge and Random Forest-Based Metric for Evaluating MT in Indigenous Languages
Venue: arXiv cs.CL 2025
Year: 2025

This paper presents the winning submission of the RaaVa team to the AmericasNLP 2025 Shared Task 3 on Automatic Evaluation Metrics for Machine Translation (MT) into Indigenous Languages of America, where our system ranked first overall based on average Pearson correlation with the human annotations. We introduce Feature-Union Scorer (FUSE) for Evaluation, FUSE integrates Ridge regression and Gradient Boosting to model translation quality. In addition to FUSE, we explore five alternative approaches leveraging different combinations of linguistic similarity features and learning paradigms. FUSE Score highlights the effectiveness of combining lexical, phonetic, semantic, and fuzzy token similarity with learning-based modeling to improve MT evaluation for morphologically rich and low-resource languages. MT into Indigenous languages poses unique challenges due to polysynthesis, complex morphology, and non-standardized orthography. Conventional automatic metrics such as BLEU, TER, and ChrF often fail to capture deeper aspects like semantic adequacy and fluency. Our proposed framework, formerly referred to as FUSE, incorporates multilingual sentence embeddings and phonological encodings to better align with human evaluation. We train supervised models on human-annotated development sets and evaluate held-out test data. Results show that FUSE consistently achieves higher Pearson and Spearman correlations with human judgments, offering a robust and linguistically informed solution for MT evaluation in low-resource settings.
Opioid Named Entity Recognition (ONER-2025) from Reddit
Venue: arXiv cs.CL 2025
Year: 2025

The opioid overdose epidemic remains a critical public health crisis, particularly in the United States, leading to significant mortality and societal costs. Social media platforms like Reddit provide vast amounts of unstructured data that offer insights into public perceptions, discussions, and experiences related to opioid use. This study leverages Natural Language Processing (NLP), specifically Opioid Named Entity Recognition (ONER-2025), to extract actionable information from these platforms. Our research makes four key contributions. First, we created a unique, manually annotated dataset sourced from Reddit, where users share self-reported experiences of opioid use via different administration routes. This dataset contains 331,285 tokens and includes eight major opioid entity categories. Second, we detail our annotation process and guidelines while discussing the challenges of labeling the ONER-2025 dataset. Third, we analyze key linguistic challenges, including slang, ambiguity, fragmented sentences, and emotionally charged language, in opioid discussions. Fourth, we propose a real-time monitoring system to process streaming data from social media, healthcare records, and emergency services to identify overdose events. Using 5-fold cross-validation in 11 experiments, our system integrates machine learning, deep learning, and transformer-based language models with advanced contextual embeddings to enhance understanding. Our transformer-based models (bert-base-NER and roberta-base) achieved 97% accuracy and F1-score, outperforming baselines by 10.23% (RF=0.88).
Generating Structured Plan Representation of Procedures with LLMs
Venue: arXiv cs.SE 2025
Year: 2025

In this paper, we address the challenges of managing Standard Operating Procedures (SOPs), which often suffer from inconsistencies in language, format, and execution, leading to operational inefficiencies. Traditional process modeling demands significant manual effort, domain expertise, and familiarity with complex languages like Business Process Modeling Notation (BPMN), creating barriers for non-techincal users. We introduce SOP Structuring (SOPStruct), a novel approach that leverages Large Language Models (LLMs) to transform SOPs into decision-tree-based structured representations. SOPStruct produces a standardized representation of SOPs across different domains, reduces cognitive load, and improves user comprehension by effectively capturing task dependencies and ensuring sequential integrity. Our approach enables leveraging the structured information to automate workflows as well as empower the human users. By organizing procedures into logical graphs, SOPStruct facilitates backtracking and error correction, offering a scalable solution for process optimization. We employ a novel evaluation framework, combining deterministic methods with the Planning Domain Definition Language (PDDL) to verify graph soundness, and non-deterministic assessment by an LLM to ensure completeness. We empirically validate the robustness of our LLM-based structured SOP representation methodology across SOPs from different domains and varying levels of complexity. Despite the current lack of automation readiness in many organizations, our research highlights the transformative potential of LLMs to streamline process modeling, paving the way for future advancements in automated procedure optimization.
Leaking LoRa: An Evaluation of Password Leaks and Knowledge Storage in Large Language Models
Venue: arXiv cs.CR 2025
Year: 2025

To effectively deploy Large Language Models (LLMs) in application-specific settings, fine-tuning techniques are applied to enhance performance on specialized tasks. This process often involves fine-tuning on user data data, which may contain sensitive information. Although not recommended, it is not uncommon for users to send passwords in messages, and fine-tuning models on this could result in passwords being leaked. In this study, a Large Language Model is fine-tuned with customer support data and passwords from the RockYou password wordlist using Low-Rank Adaptation (LoRA). Out of the first 200 passwords from the list, 37 were successfully recovered. Further, causal tracing is used to identify that password information is largely located in a few layers. Lastly, Rank One Model Editing (ROME) is used to remove the password information from the model, resulting in the number of passwords recovered going from 37 to 0.
Assessing Code Understanding in LLMs
Venue: arXiv cs.SE 2025
Year: 2025

We present an empirical evaluation of Large Language Models in code understanding associated with non-trivial, semantic-preserving program transformations such as copy propagation or constant folding. Our findings show that LLMs fail to judge semantic equivalence in approximately 41\% of cases when no context is provided and in 29\% when given a simple generic context. To improve accuracy, we advocate integrating LLMs with code-optimization tools to enhance training and facilitate more robust program understanding.
EMForecaster: A Deep Learning Framework for Time Series Forecasting in Wireless Networks with Distribution-Free Uncertainty Quantification
Venue: arXiv cs.LG 2025
Year: 2025

With the recent advancements in wireless technologies, forecasting electromagnetic field (EMF) exposure has become critical to enable proactive network spectrum and power allocation, as well as network deployment planning. In this paper, we develop a deep learning (DL) time series forecasting framework referred to as \textit{EMForecaster}. The proposed DL architecture employs patching to process temporal patterns at multiple scales, complemented by reversible instance normalization and mixing operations along both temporal and patch dimensions for efficient feature extraction. We augment {EMForecaster} with a conformal prediction mechanism, which is independent of the data distribution, to enhance the trustworthiness of model predictions via uncertainty quantification of forecasts. This conformal prediction mechanism ensures that the ground truth lies within a prediction interval with target error rate $α$, where $1-α$ is referred to as coverage. However, a trade-off exists, as increasing coverage often results in wider prediction intervals. To address this challenge, we propose a new metric called the \textit{Trade-off Score}, that balances trustworthiness of the forecast (i.e., coverage) and the width of prediction interval. Our experiments demonstrate that EMForecaster achieves superior performance across diverse EMF datasets, spanning both short-term and long-term prediction horizons. In point forecasting tasks, EMForecaster substantially outperforms current state-of-the-art DL approaches, showing improvements of 53.97\% over the Transformer architecture and 38.44\% over the average of all baseline models. EMForecaster also exhibits an excellent balance between prediction interval width and coverage in conformal forecasting, measured by the tradeoff score, showing marked improvements of 24.73\% over the average baseline and 49.17\% over the Transformer architecture.
Why risk matters for protein binder design
Venue: arXiv cs.LG 2025
Year: 2025

Bayesian optimization (BO) has recently become more prevalent in protein engineering applications and hence has become a fruitful target of benchmarks. However, current BO comparisons often overlook real-world considerations like risk and cost constraints. In this work, we compare 72 model combinations of encodings, surrogate models, and acquisition functions on 11 protein binder fitness landscapes, specifically from this perspective. Drawing from the portfolio optimization literature, we adopt metrics to quantify the cold-start performance relative to a random baseline, to assess the risk of an optimization campaign, and to calculate the overall budget required to reach a fitness threshold. Our results suggest the existence of Pareto-optimal models on the risk-performance axis, the shift of this preference depending on the landscape explored, and the robust correlation between landscape properties such as epistasis with the average and worst-case model performance. They also highlight that rigorous model selection requires substantial computational and statistical efforts.
Few-Shot Generation of Brain Tumors for Secure and Fair Data Sharing
Venue: arXiv cs.CV 2025
Year: 2025

Leveraging multi-center data for medical analytics presents challenges due to privacy concerns and data heterogeneity. While distributed approaches such as federated learning has gained traction, they remain vulnerable to privacy breaches, particularly in sensitive domains like medical imaging. Generative models, such as diffusion models, enhance privacy by synthesizing realistic data. However, they are prone to memorization, especially when trained on small datasets. This study proposes a decentralized few-shot generative model (DFGM) to synthesize brain tumor images while fully preserving privacy. DFGM harmonizes private tumor data with publicly shareable healthy images from multiple medical centers, constructing a new dataset by blending tumor foregrounds with healthy backgrounds. This approach ensures stringent privacy protection and enables controllable, high-quality synthesis by preserving both the healthy backgrounds and tumor foregrounds. We assess DFGM's effectiveness in brain tumor segmentation using a UNet, achieving Dice score improvements of 3.9% for data augmentation and 4.6% for fairness on a separate dataset.
From Solo to Social: Exploring the Dynamics of Player Cooperation in a Co-located Cooperative Exergame
Venue: arXiv cs.HC 2025
Year: 2025

Digital games offer rich social experiences and promote valuable skills, but they fall short in addressing physical inactivity. Exergames, which combine exercise with gameplay, have the potential to tackle this issue. However, current exergames are primarily single-player or competitive. To explore the social benefits of cooperative exergaming, we designed a custom co-located cooperative exergame that features three distinct forms of cooperation: Free (baseline), Coupled, and Concurrent. We conducted a within-participants, mixed-methods study (N = 24) to evaluate these designs and their impact on players' enjoyment, motivation, and performance. Our findings reveal that cooperative play improves social experiences. It drives increased team identification and relatedness. Furthermore, our qualitative findings support cooperative exergame play. This has design implications for creating exergames that effectively address players' exercise and social needs. Our research contributes guidance for developers and researchers who want to create more socially enriching exergame experiences.
Discriminative Subspace Emersion from learning feature relevances across different populations
Venue: arXiv cs.LG 2025
Year: 2025

In a given classification task, the accuracy of the learner is often hampered by finiteness of the training set, high-dimensionality of the feature space and severe overlap between classes. In the context of interpretable learners, with (piecewise) linear separation boundaries, these issues can be mitigated by careful construction of optimization procedures and/or estimation of relevant features for the task. However, when the task is shared across two disjoint populations the main interest is shifted towards estimating a set of features that discriminate the most between the two, when performing classification. We propose a new Discriminative Subspace Emersion (DSE) method to extend subspace learning toward a general relevance learning framework. DSE allows us to identify the most relevant features in distinguishing the classification task across two populations, even in cases of high overlap between classes. The proposed methodology is designed to work with multiple sets of labels and is derived in principle without being tied to a specific choice of base learner. Theoretical and empirical investigations over synthetic and real-world datasets indicate that DSE accurately identifies a common subspace for the classification across different populations. This is shown to be true for a surprisingly high degree of overlap between classes.
Beamforming Design for Continuous Aperture Array (CAPA)-Based MIMO Systems
Venue: arXiv cs.IT 2025
Year: 2025

An efficient beamforming design is proposed for continuous aperture array (CAPA)-based point-to-point multiple-input multiple-output (MIMO) systems. In contrast to conventional spatially discrete array (SPDA)-MIMO systems, whose optimal beamforming can be obtained using singular-value decomposition, CAPA-MIMO systems require solving the eigendecomposition of a Hermitian kernel operator, which is computationally prohibitive. To address this challenge, an explicit closed-form expression for the achievable rate of CAPA-MIMO systems is first derived as a function of the continuous transmit beamformer. Subsequently, an iterative weighted minimum mean-squared error (WMMSE) algorithm is proposed, directly addressing the CAPA-MIMO beamforming optimization without discretization approximation. Closed-form updates for each iteration of the WMMSE algorithm are derived via the calculus of variations (CoV) method. For low-complexity implementation, an equivalent matrix-based iterative solution is introduced using Gauss-Legendre quadrature. Our numerical results demonstrate that 1) CAPA-MIMO achieves substantial performance gain over the SPDA-MIMO, 2) the proposed WMMSE algorithm enhances performance while significantly reducing computational complexity compared to state-of-the-art Fourier-based approaches, and 3) the proposed WMMSE algorithm enables practical realization of parallel, non-interfering transmissions.
SmartScan: An AI-based Interactive Framework for Automated Region Extraction from Satellite Images
Venue: arXiv cs.CV 2025
Year: 2025

The deployment of a continuous methane monitoring system requires determining the optimal number and placement of fixed sensors. However, planning is labor-intensive, requiring extensive site setup and iteration to meet client restrictions. This challenge is amplified when evaluating multiple sites, limiting scalability. To address this, we introduce SmartScan, an AI framework that automates data extraction for optimal sensor placement. SmartScan identifies subspaces of interest from satellite images using an interactive tool to create facility-specific constraint sets efficiently. SmartScan leverages the Segment Anything Model (SAM), a prompt-based transformer for zero-shot segmentation, enabling subspace extraction without explicit training. It operates in two modes: (1) Data Curation Mode, where satellite images are processed to extract high-quality subspaces using an interactive prompting system for SAM, and (2) Autonomous Mode, where user-curated prompts train a deep learning network to replace manual prompting, fully automating subspace extraction. The interactive tool also serves for quality control, allowing users to refine AI-generated outputs and generate additional constraint sets as needed. With its AI-driven prompting mechanism, SmartScan delivers high-throughput, high-quality subspace extraction with minimal human intervention, enhancing scalability and efficiency. Notably, its adaptable design makes it suitable for extracting regions of interest from ultra-high-resolution satellite imagery across various domains.
PneuDrive: An Embedded Pressure Control System and Modeling Toolkit for Large-Scale Soft Robots
Venue: arXiv cs.RO 2025
Year: 2025

In this paper, we present a modular pressure control system called PneuDrive that can be used for large-scale, pneumatically-actuated soft robots. The design is particularly suited for situations which require distributed pressure control and high flow rates. Up to four embedded pressure control modules can be daisy-chained together as peripherals on a robust RS-485 bus, enabling closed-loop control of up to 16 valves with pressures ranging from 0-100 psig (0-689 kPa) over distances of more than 10 meters. The system is configured as a C++ ROS node by default. However, independent of ROS, we provide a Python interface with a scripting API for added flexibility. We demonstrate our implementation of PneuDrive through various trajectory tracking experiments for a three-joint, continuum soft robot with 12 different pressure inputs. Finally, we present a modeling toolkit with implementations of three dynamic actuation models, all suitable for real-time simulation and control. We demonstrate the use of this toolkit in customizing each model with real-world data and evaluating the performance of each model. The results serve as a reference guide for choosing between several actuation models in a principled manner. A video summarizing our results can be found here: https://bit.ly/3QkrEqO.
Opportunistic Screening for Pancreatic Cancer using Computed Tomography Imaging and Radiology Reports
Venue: arXiv cs.LG 2025
Year: 2025

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer, with most cases diagnosed at stage IV and a five-year overall survival rate below 5%. Early detection and prognosis modeling are crucial for improving patient outcomes and guiding early intervention strategies. In this study, we developed and evaluated a deep learning fusion model that integrates radiology reports and CT imaging to predict PDAC risk. The model achieved a concordance index (C-index) of 0.6750 (95% CI: 0.6429, 0.7121) and 0.6435 (95% CI: 0.6055, 0.6789) on the internal and external dataset, respectively, for 5-year survival risk estimation. Kaplan-Meier analysis demonstrated significant separation (p<0.0001) between the low and high risk groups predicted by the fusion model. These findings highlight the potential of deep learning-based survival models in leveraging clinical and imaging data for pancreatic cancer.
Digital Twins in Biopharmaceutical Manufacturing: Review and Perspective on Human-Machine Collaborative Intelligence
Venue: arXiv cs.HC 2025
Year: 2025

The biopharmaceutical industry is increasingly developing digital twins to digitalize and automate the manufacturing process in response to the growing market demands. However, this shift presents significant challenges for human operators, as the complexity and volume of information can overwhelm their ability to manage the process effectively. These issues are compounded when digital twins are designed without considering interaction and collaboration with operators, who are responsible for monitoring processes and assessing situations, particularly during abnormalities. Our review of current trends in biopharma digital twin development reveals a predominant focus on technology and often overlooks the critical role of human operators. To bridge this gap, this article proposes a collaborative intelligence framework that emphasizes the integration of operators with digital twins. Approaches to system design that can enhance operator trust and human-machine interface usability are presented. Moreover, innovative training programs for preparing operators to understand and utilize digital twins are discussed. The framework outlined in this article aims to enhance collaboration between operators and digital twins effectively by using their full capabilities to boost resilience and productivity in biopharmaceutical manufacturing.